Chlorine in PDB 8f4g: Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution, PDB code: 8f4g was solved by A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.573, 222.915, 309.999, 90, 90, 90
R / Rfree (%) 18 / 22.3

Other elements in 8f4g:

The structure of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 70 atoms
Manganese (Mn) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution (pdb code 8f4g). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution, PDB code: 8f4g:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8f4g

Go back to Chlorine Binding Sites List in 8f4g
Chlorine binding site 1 out of 4 in the Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:27.0
occ:1.00
 O D:HOH592 3.0 30.3 1.0
NZ D:LYS317 3.2 29.7 1.0
N A:GLU333 3.3 26.5 0.5
N A:GLU333 3.3 30.6 0.4
O A:HOH720 3.3 27.0 1.0
OD1 A:ASN181 3.3 27.1 0.5
N A:GLU333 3.4 28.3 0.1
OD1 A:ASN181 3.4 31.6 0.1
OD1 A:ASN181 3.4 31.7 0.4
CB A:HIS332 3.6 27.9 0.1
CA A:HIS332 3.6 27.9 0.5
CA A:HIS332 3.6 31.3 0.1
CB A:HIS332 3.7 26.4 0.5
CA A:HIS332 3.7 30.5 0.4
CB A:HIS332 3.8 26.7 0.4
CG A:GLU333 3.9 27.0 0.5
CG A:GLU333 3.9 29.6 0.4
CG A:GLU333 3.9 26.1 0.1
C A:HIS332 3.9 29.0 0.5
C A:HIS332 4.0 28.9 0.1
C A:HIS332 4.0 30.5 0.4
CE D:LYS317 4.1 23.2 1.0
ND2 A:ASN181 4.2 23.6 0.1
CG A:ASN181 4.2 27.2 0.1
CG A:ASN181 4.2 24.0 0.5
CA A:GLU333 4.2 29.1 0.4
O A:HOH727 4.2 29.1 1.0
CA A:GLU333 4.2 30.2 0.5
CG2 A:VAL185 4.3 25.7 0.4
CG2 A:VAL185 4.3 23.2 0.5
CG A:ASN181 4.3 28.5 0.4
ND2 A:ASN181 4.3 24.5 0.5
CA A:GLU333 4.3 28.4 0.1
ND2 A:ASN181 4.4 25.2 0.4
CG2 A:VAL185 4.4 28.2 0.1
CD2 D:LEU321 4.4 24.3 1.0
O A:HOH780 4.4 28.7 1.0
CD1 D:LEU321 4.4 24.6 1.0
CB D:LYS317 4.6 25.1 1.0
CG A:HIS332 4.6 27.2 0.1
CB A:GLU333 4.7 28.2 0.4
CB A:GLU333 4.7 26.4 0.5
CG D:LEU321 4.7 26.1 1.0
CG A:HIS332 4.7 29.4 0.5
CB A:GLU333 4.7 26.6 0.1
CG D:LYS317 4.8 28.1 1.0
CG A:HIS332 4.8 31.5 0.4
OE2 A:GLU333 4.8 27.8 0.1
CD A:GLU333 4.8 28.4 0.1
O D:HOH525 4.9 30.3 1.0
CD2 A:HIS332 4.9 29.5 0.1
CD A:GLU333 4.9 30.6 0.4
CD A:GLU333 4.9 27.2 0.5
N A:HIS332 4.9 24.0 0.5
N A:HIS332 5.0 26.5 0.1
CD2 A:HIS332 5.0 29.1 0.5

Chlorine binding site 2 out of 4 in 8f4g

Go back to Chlorine Binding Sites List in 8f4g
Chlorine binding site 2 out of 4 in the Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:28.7
occ:1.00
 O A:HOH788 2.9 31.3 1.0
O C:HOH686 3.1 28.5 1.0
N A:ASN338 3.2 30.3 0.4
N C:GLU354 3.3 30.1 0.1
N A:ASN338 3.3 27.5 0.1
N A:ASN338 3.3 28.2 0.5
N C:GLU354 3.3 27.5 0.5
N C:GLU354 3.4 28.7 0.4
CA A:HIS337 3.6 28.2 0.5
CA A:HIS337 3.7 29.0 0.4
CA A:HIS337 3.7 30.2 0.1
CD2 A:PHE339 3.8 29.2 0.4
CA C:GLY353 3.8 26.4 0.1
CA C:GLY353 3.8 27.1 0.5
N A:PHE339 3.8 31.7 0.4
N A:PHE339 3.8 29.1 0.1
CA C:GLY353 3.8 27.3 0.4
N A:PHE339 3.9 25.7 0.5
CD2 A:PHE339 3.9 27.8 0.1
CD2 A:PHE339 3.9 25.8 0.5
C A:HIS337 3.9 29.1 0.4
C A:HIS337 4.0 28.4 0.5
C A:HIS337 4.0 29.2 0.1
C C:GLY353 4.0 29.8 0.1
C C:GLY353 4.0 27.8 0.5
CB C:GLU354 4.1 31.6 0.1
CB C:GLU354 4.1 28.4 0.5
O A:ALA336 4.1 31.5 0.5
CA A:ASN338 4.1 26.7 0.4
C C:GLY353 4.2 29.1 0.4
CB A:HIS337 4.2 25.6 0.5
O A:ALA336 4.2 33.0 0.1
CB A:HIS337 4.2 28.9 0.1
O A:ALA336 4.2 32.8 0.4
CB A:HIS337 4.2 29.1 0.4
CB C:GLU354 4.2 30.2 0.4
CA C:GLU354 4.2 32.5 0.1
CA A:ASN338 4.3 27.9 0.1
CA C:GLU354 4.3 27.6 0.5
CA A:ASN338 4.3 25.9 0.5
CB A:PHE339 4.4 28.5 0.4
CB A:ASN338 4.4 31.3 0.4
CA C:GLU354 4.4 30.6 0.4
CB A:PHE339 4.4 26.3 0.5
C A:ASN338 4.4 28.2 0.4
CG A:PHE339 4.4 31.0 0.4
O C:HOH697 4.5 26.3 1.0
CB A:PHE339 4.5 27.2 0.1
O C:HOH734 4.5 34.2 1.0
C A:ASN338 4.5 28.5 0.1
CE2 A:PHE339 4.5 29.5 0.4
C A:ASN338 4.5 27.2 0.5
CB A:ASN338 4.5 32.4 0.1
CG A:PHE339 4.6 27.9 0.5
CG A:PHE339 4.6 29.8 0.1
CB A:ASN338 4.6 29.0 0.5
CA A:PHE339 4.6 29.8 0.4
O A:PHE339 4.7 30.1 0.4
O A:PHE339 4.7 27.2 0.5
CA A:PHE339 4.7 29.1 0.1
CA A:PHE339 4.7 27.7 0.5
CE2 A:PHE339 4.7 27.8 0.1
O A:PHE339 4.7 28.9 0.1
CG C:GLU354 4.7 29.5 0.4
CE2 A:PHE339 4.7 26.4 0.5
N A:HIS337 4.7 28.4 0.5
N A:HIS337 4.8 28.1 0.4
N C:THR355 4.8 30.1 0.1
CG C:GLU354 4.8 31.7 0.1
N A:HIS337 4.8 29.6 0.1
N C:THR355 4.9 27.8 0.5
C A:ALA336 4.9 28.7 0.5
N C:THR355 4.9 28.0 0.4
CG A:HIS337 4.9 28.0 0.5
CD2 A:HIS337 4.9 27.5 0.5
CD2 A:HIS337 4.9 29.6 0.1
CG A:HIS337 4.9 28.5 0.1
CD2 A:HIS337 4.9 26.6 0.4
C A:ALA336 5.0 30.0 0.4
CG A:HIS337 5.0 29.2 0.4
O C:GLY352 5.0 30.7 1.0
C A:ALA336 5.0 31.6 0.1
CG A:ASN338 5.0 33.1 0.4

Chlorine binding site 3 out of 4 in 8f4g

Go back to Chlorine Binding Sites List in 8f4g
Chlorine binding site 3 out of 4 in the Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl604

b:29.8
occ:1.00
 O d:HOH560 3.1 26.7 1.0
O a:HOH715 3.2 26.6 1.0
NZ d:LYS317 3.2 31.9 1.0
N a:GLU333 3.3 26.6 0.5
N a:GLU333 3.3 29.6 0.1
N a:GLU333 3.3 29.1 0.4
OD1 a:ASN181 3.4 29.4 0.5
OD1 a:ASN181 3.5 32.4 0.4
OD1 a:ASN181 3.5 30.5 0.1
CB a:HIS332 3.5 30.0 0.1
CA a:HIS332 3.6 30.2 0.1
CA a:HIS332 3.6 29.7 0.5
CB a:HIS332 3.7 25.5 0.5
CA a:HIS332 3.7 28.2 0.4
CB a:HIS332 3.8 28.0 0.4
CE d:LYS317 3.9 28.0 1.0
C a:HIS332 3.9 28.2 0.5
CG a:GLU333 4.0 30.1 0.4
CG a:GLU333 4.0 25.8 0.5
C a:HIS332 4.0 28.9 0.1
C a:HIS332 4.0 29.3 0.4
CG a:GLU333 4.1 28.5 0.1
ND2 a:ASN181 4.2 22.5 0.4
CD2 d:LEU321 4.2 27.0 1.0
CA a:GLU333 4.3 25.9 0.5
CA a:GLU333 4.3 29.4 0.4
CG a:ASN181 4.3 28.2 0.4
CG a:ASN181 4.3 27.4 0.5
ND2 a:ASN181 4.3 24.5 0.1
CA a:GLU333 4.3 28.4 0.1
CG a:ASN181 4.3 28.7 0.1
CG2 a:VAL185 4.3 28.2 0.5
O d:HOH542 4.3 28.1 1.0
ND2 a:ASN181 4.3 24.5 0.5
CG2 a:VAL185 4.3 25.2 0.4
CG2 a:VAL185 4.4 26.9 0.1
O a:HOH770 4.4 32.7 1.0
CD1 d:LEU321 4.4 30.4 1.0
CB d:LYS317 4.5 26.8 1.0
CG a:HIS332 4.5 28.2 0.1
CG a:HIS332 4.7 28.2 0.5
CB a:GLU333 4.7 28.4 0.4
CB a:GLU333 4.7 25.7 0.5
CG a:HIS332 4.8 28.1 0.4
CB a:GLU333 4.8 29.6 0.1
CD2 a:HIS332 4.8 32.1 0.1
O d:LYS317 4.8 30.6 1.0
CG d:LYS317 4.9 24.6 1.0
CD a:GLU333 4.9 29.8 0.4
N a:HIS332 4.9 23.6 0.5
CD2 a:HIS332 5.0 25.7 0.5
O d:HOH511 5.0 27.8 1.0
N a:HIS332 5.0 25.8 0.1
CG d:LEU321 5.0 33.1 1.0

Chlorine binding site 4 out of 4 in 8f4g

Go back to Chlorine Binding Sites List in 8f4g
Chlorine binding site 4 out of 4 in the Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rt Xfel Structure of Photosystem II 730 Microseconds After the Third Illumination at 2.03 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl605

b:30.8
occ:1.00
 O c:HOH696 3.0 30.4 1.0
N a:ASN338 3.1 26.6 0.5
N a:ASN338 3.2 27.4 0.1
N a:ASN338 3.2 28.2 0.4
O a:HOH712 3.2 33.0 1.0
N c:GLU354 3.4 31.2 0.4
N c:GLU354 3.4 29.1 0.5
N c:GLU354 3.4 31.2 0.1
CA a:HIS337 3.6 26.5 0.5
N a:PHE339 3.6 25.2 0.5
CA a:HIS337 3.6 26.4 0.4
CA a:HIS337 3.7 25.8 0.1
N a:PHE339 3.7 28.9 0.4
N a:PHE339 3.7 28.8 0.1
CD2 a:PHE339 3.8 26.4 0.5
CD2 a:PHE339 3.8 29.9 0.4
C a:HIS337 3.8 30.4 0.5
CD2 a:PHE339 3.8 30.5 0.1
C a:HIS337 3.9 32.8 0.4
C a:HIS337 3.9 31.2 0.1
CA c:GLY353 3.9 27.9 0.4
CA c:GLY353 4.0 27.0 0.1
CA c:GLY353 4.0 28.9 0.5
CA a:ASN338 4.1 29.2 0.5
CB c:GLU354 4.1 30.1 0.4
CB c:GLU354 4.1 28.2 0.5
CA a:ASN338 4.1 27.8 0.1
O a:ALA336 4.1 29.1 0.1
CA a:ASN338 4.1 27.9 0.4
CB c:GLU354 4.1 27.9 0.1
O a:ALA336 4.1 32.4 0.4
CB a:HIS337 4.1 26.8 0.5
C c:GLY353 4.1 28.6 0.4
O a:ALA336 4.2 32.6 0.5
C c:GLY353 4.2 29.1 0.1
C c:GLY353 4.2 27.9 0.5
CB a:HIS337 4.2 29.9 0.4
CB a:HIS337 4.3 27.6 0.1
C a:ASN338 4.3 29.8 0.5
CA c:GLU354 4.3 28.5 0.4
CA c:GLU354 4.3 27.9 0.5
CB a:ASN338 4.3 29.5 0.1
CB a:PHE339 4.3 30.0 0.4
CB a:PHE339 4.3 28.6 0.5
CB a:PHE339 4.4 31.1 0.1
CA c:GLU354 4.4 27.8 0.1
CB a:ASN338 4.4 26.5 0.5
CB a:ASN338 4.4 28.6 0.4
CG a:PHE339 4.4 29.4 0.4
C a:ASN338 4.4 30.8 0.1
C a:ASN338 4.4 30.5 0.4
CG a:PHE339 4.4 27.9 0.5
O a:PHE339 4.4 30.8 0.5
CG a:PHE339 4.5 29.8 0.1
CA a:PHE339 4.5 29.8 0.5
O a:PHE339 4.5 35.6 0.4
O c:HOH668 4.5 29.1 1.0
CE2 a:PHE339 4.5 27.9 0.4
O a:PHE339 4.5 32.2 0.1
CE2 a:PHE339 4.5 26.0 0.5
CA a:PHE339 4.6 31.6 0.4
CA a:PHE339 4.6 30.9 0.1
CE2 a:PHE339 4.6 25.9 0.1
CG c:GLU354 4.7 27.8 0.4
O a:HOH799 4.7 30.9 1.0
N a:HIS337 4.7 25.9 0.5
N a:HIS337 4.7 28.9 0.4
CD2 a:HIS337 4.8 29.1 0.1
N a:HIS337 4.8 27.1 0.1
CD2 a:HIS337 4.8 30.4 0.4
N c:THR355 4.9 27.7 0.4
N c:THR355 4.9 29.3 0.5
CG a:HIS337 4.9 29.1 0.5
C a:ALA336 4.9 30.7 0.4
CG a:HIS337 4.9 29.0 0.1
C a:ALA336 4.9 29.5 0.5
CD2 a:HIS337 4.9 28.2 0.5
CG a:HIS337 4.9 29.8 0.4
CG c:GLU354 4.9 29.5 0.1
CG a:ASN338 4.9 29.1 0.1
C a:ALA336 4.9 30.2 0.1
C a:PHE339 4.9 30.0 0.5
NE2 c:GLN313 4.9 27.9 1.0
N c:THR355 5.0 27.9 0.1
O c:HOH701 5.0 29.9 1.0
C a:PHE339 5.0 31.8 0.4

Reference:

A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra. Structural Evidence For Intermediates During O2 Formation in Photosystem II To Be Published.
Page generated: Tue Jul 30 09:14:09 2024

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